run.sh

#!/bin/bash
# Singularity App runscript
# Author: MB
# Date: 5.11.2019
#
# Executes either the app or the executable
#
usage(){
    echo "Singularity Container"
	if [[ -f /.singularity.d/runscript.help ]]; then
		cat /.singularity.d/runscript.help
	else
		if [[ -f /etc/os-release ]]; then
			echo $(grep PRETTY_NAME= /etc/os-release | sed 's/PRETTY_NAME=//')
		elif [[ -f /etc/centos-release ]]; then
			echo $(cat /etc/centos-release)
		else
			echo $(uname -a)
		fi
	fi
	if [[ -d /scif/apps ]]; then
		echo "SCIF (Apps): " $(ls /scif/apps)
	fi
}

infos(){
	if [[ -f /.singularity.d/labels.json ]]; then
		python <<EOF
import json
data=json.loads(open('/.singularity.d/labels.json').read())
n=max(map(len, data.keys()))
format='%-'+str(n)+'s : %s'
for i in sorted(data.keys()):
	print(format % (i,data[i]))
EOF
	fi
}


if [ $# -gt 0 ]; then
	if [[ "$1" == "--help" ]] || [[ "$1" == "-h" ]]; then
		usage
		exit
	fi
	if [[ "$1" == "--info" ]]; then
		infos
		exit
	fi

	if [[ -d /scif/apps ]]; then
		echo $(ls /scif/apps) | grep $1 > /dev/null
		if [ $? -eq 0 ]; then
			name=$1
			echo "Launching app: $name"
			shift
			exec /scif/apps/${name}/scif/runscript "$@"
		else
			echo "Executing: $@"
			exec "$@"
		fi
	else
		echo "Executing: $@"
		exec "$@"
    fi
else
    usage
    echo "Bye Bye"
fi